/*
 * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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 * THE SOFTWARE.
 */
package org.ncic.bioinfo.sparkseq.algorithms.walker.baserecalibrator.covariate;

/**
 * Author: wbc
 */
public class RepeatUnitAndLengthCovariate extends RepeatCovariate {

    protected String getCovariateValueFromUnitAndLength(final byte[] repeatFromUnitAndLength, final int repeatLength) {
        return new String(repeatFromUnitAndLength) + String.format("%d",repeatLength);
    }

    @Override
    public synchronized int maximumKeyValue() {
        // Synchronized so that we don't query table size while the tables are being updated
        //return repeatLookupTable.size() - 1;
        // max possible values of covariate: for repeat unit, length is up to MAX_STR_UNIT_LENGTH,
        // so we have 4^MAX_STR_UNIT_LENGTH * MAX_REPEAT_LENGTH possible values
        return (1<<(2*MAX_STR_UNIT_LENGTH)) * MAX_REPEAT_LENGTH +1;
    }

}
